|Waterhouse, A Mermaid|
The idea of Mendelian inheritance, which is widely extended to the vast majority of gene-trait relationships that clearly are not following the monk's principles, is of discrete states one of which dominates in their various combinations. This was (and is) extended to evolution, with our grossly inadequate 'winner take all', 'survival of the fittest' notion of one best -- fitness-wise dominant -- variant that natural selection favored into success just as surely as a dominant allele was favored ineluctably into manifestation in the organism.
But if you think of the other properties of life, which we center our book around and will briefly name here, you might ask how Mendelian thinking, which only by deep contortions can be related to those principles, could ever have taken hold, unless it's by what amounts to an ideology, a takeover of a certain highly deterministic, simplistic view of the living world--a view that simply, for decades, wrote off into alleged irrelevance the actual way in which organisms work.
Sequestration and modularity
From DNA on up, life is organized as hierarchically nested partially sequestered units. DNA has functional sequence elements arranged together along chromosomes, but partially isolated in that they can serve their individual functions. The units (such as amino acid codons) are repeated many times. Proteins have partly separated functional units, too. Cells are packaged units that have many different partially isolated subunits within them, such as organelles like mitochodria, isolated areas like the nucleus, and local differences in what is present in the cell membrane (e.g., a cell may have a front and back end, so to speak).
An organism (or even collections of organisms as in bacterial biofilms) is made of large numbers of cells. These are repeated units that communicate with each other via combinations of signaling and other molecules, and this is what leads them to express particular, context-dependent sets of genes. So that they are repeated, but different. This process occurs hierarchically during development, and in response to environmental changes during life. An organism is divided into organs and organ systems, like brain, heart and vessels, digestive organs, and so on.
Organs are made of nested, repeated units. Intestines are segmented along their length, and their surface is littered with repeated structures called 'villi'. Skeletons are made of repeated, partially different but interaction bones. Trees are made of leaves and so on. Plants and animals alike are constructed by repetition and branching.
Yet, importantly, each organism has only the one genome that it inherited from its parents! So the same genome makes brains and braincases, that are as different from each other as any two things in all of life.
These processes are both qualitative: each leaf or bone is a separate structure; and quantitative: each such structure is somewhat different. This is the natural variation that is the material on which evolution can work.
If you just think about this, you would have to wonder how it could be brought about by Mendelian inheritance. How could just two states at a single gene be responsible for such complexity and quantitative internal organization?
It is perhaps easier to see how breaking a gene could cause a major state change, and thus a normal and dead alternative at a gene could be manifest in Mendelian inheritance terms. Or if the trait is very close to a protein coded by a single gene, two major alleles (variants) at that gene could have big differences (yellow vs green peas, for example). But as a rule, Mendelian inheritance makes little sense. Partly that's because, as mentioned in earlier parts of this series, we confuse inheritance of traits with inheritance of genes. Genes--specific stretches of DNA--are clearly inherited in a Mendelian way (with some exceptions that don't matter in this context here). But traits generally are not.
The reason for all of this is that the basic principles of life, that include the above descriptions (see our book for detailed discussion in this context), involve cooperation--that is, co-operation or contemporary interaction--among many different elements, each of them variable in a population. What an individual inherits are sets of genomic variants from its parents. The traits an individual manifests are the net results of these variants acting in the particular environments in which they find themselves.